Introduction
ssGSEA taskforce is a standalone desktop software for running Single Sample Gene Enrichment Analysis (ssGSEA) and analyzing ssGSEA results. This tutorial is intended for users who would like to quickly get started by installing the software, running ssGSEA analysis and analyzing their results.
For support, bug reports and updates, please visit:
https://github.com/ayguno
Download and Software Installation
Currently only available for WINDOWS
The latest version of the software is available to download from the following URL:
DOWNLOAD ssGSEA Taskforce V.0.1
Download the ssGSEAtaskforce_setup.exe file into your computer and double click to start the install wizard:
Click to Next:
By default, the software will be installed into your C: drive. Click to INSTALL to continue.
Complete installation:
You should see the ssGSEA icon on your desktop.
Main Menu
Click to run the software. A portable version of Google Chrome will open. You will notice it takes some time to load the software in the first instance,as it may ask you to load some extensions of the Adobe Reader in a separate tab. You can ignore and close that tab. The actual software will appear in the tab with a default IP address/port: //127.0.0.1:8888/
The main menu will look like:
Run ssGSEA
Loading gene expression data and choosing parameters
Click to Run ssGSEA to open ssGSEA run wizard:
- Upload your expression data set.
- Provide a useful title for your project.
- Choose your parameters: various tips are provided on how to choose your parameters.
- YOU MUST PROVIDE A VALID E-MAIL ADDRESS: if you would like to receive your results.
The ssGSEA run console
Once your parameters are ready, click to move to next stage:
Here you will be asked to review the parameters you defined. Since ssGSEA runs are computationally intensive, it is generally a good idea to check the parameters carefully before starting the run. If you wish to refine your parameters, click back and you will be redirected to the refine parameters page.
Once you are ready, click to run ssGSEA to start the run.
DO NOT CLOSE YOUR BROWSER WHEN YOUR ANALYSIS IS RUNNING!
You will notice the real-time run console will start working. It will start by printing the unique JOB-ID for your task: keep this for your records.
If you provided your e-mail address:
- You will receive an e-mail immediately after you started the run, which will also include your unique ssGSEA JOB-ID.
- Once your task is completed, you will again receive an e-mail notification, which will include your results files along with the parameters you used as attachments.
Once your run is completed, you will be directed back to the main menu.
Analyze ssGSEA
Click to Analyze ssGSEA to open analysis tools:
Retrieve your results
Your results will be accessible to you under the unique JOB-ID you were provided during the run. Just use the pull-down menu to choose the run you are interested in analyzing.
Click: Retrieve Results
Manually load your results files
Alternatively, you can upload the results files yourself. First click to Load the results on the right panel radio button, then upload your files on the right. Make sure you upload the various files correctly.
Once you uploaded the files, click: Submit your files
Acknowledgements
I would like to thank Karsten Krug for providing the source code for the sGSEAplot and D.R. Mani for providing the ssGSEA script.
References
GSEA algorithm was originally developed by Aravind Subramanian. ssGSEA algorithm is a modified version developed by Pablo Tamayo and modified by D.R. Mani.
Key references:
Abazeed, M. E., Adams, D. J., Hurov, K. E., Tamayo, P., Creighton, C. J., Sonkin, D., et al. (2013).Integrative Radiogenomic Profiling of Squamous Cell Lung Cancer. Cancer Research, 73(20).
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., et al. (2005),Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102(43).